Would think keep it covered for a couple of reasons: 1) at part throttle air from the 2 front intakes is slightly pressurized and actually flows out of the hood vent (at full throttle the hood vent is an intake due to vacuum effect), 2) leaving it open would disrupt the airflow in the air box 3) there's more potential for heat from the engine increasing intake temps.

This is a quote from the M3 Aftersales Training Manual: "To optimize air resistance, no air-mass sensor is installed in the intake area. The air flow is determined using a model- based calculation from the aperture of the throttle valve assemblies and the idle speed actuator, the VANOS adjustment position, the engine speed, the air temperature and the atmospheric pressure."

ie sounds like the engineers designed the closed airbox the way it did for optimizing flow.